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Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium Mark de Been a , Mette Pinholt b , c , Janetta Top a , Stefan Bletz d , Alexander Mellmann d , Willem van Schaik a , Ellen Brouwer a , Malbert Rogers a , Yvette Kraat e , Marc Bonten a , Jukka Corander f , Henrik Westh b , c , Dag Harmsen g and Rob J. L. Willems a a Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands b Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark c Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark d Institute of Hygiene, University of Münster, Münster, Germany e Department of Microbiology and Infection Prevention, Atrium-Orbis Medical Center, Sittard, the Netherlands f Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland g Department for Periodontology, University of Münster, Münster, Germany K. C. Carroll , Editor ABSTRACT Enterococcus faecium , a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium . However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium . cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

Dec 1, 2015

Abstract

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium Mark de Been a , Mette Pinholt b , c , Janetta Top a , Stefan Bletz d , Alexander Mellmann d , Willem van Schaik a , Ellen Brouwer a , Malbert Rogers a , Yvette Kraat e , Marc Bonten a , Jukka Corander f , Henrik Westh b , c , Dag Harmsen g and Rob J. L. Willems a a Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands b Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark c Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark d Institute of Hygiene, University of Münster, Münster, Germany e Department of Microbiology and Infection Prevention, Atrium-Orbis Medical Center, Sittard, the Netherlands f Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland g Department for Periodontology, University of Münster, Münster, Germany K. C. Carroll , Editor ABSTRACT Enterococcus faecium , a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium . However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium . cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.

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References (44)

Publisher
American Society For Microbiology
Copyright
Copyright © 2015 by the American society for Microbiology.
ISSN
0095-1137
eISSN
1098-660X
DOI
10.1128/JCM.01946-15
pmid
26400782
Publisher site
See Article on Publisher Site

Abstract

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium Mark de Been a , Mette Pinholt b , c , Janetta Top a , Stefan Bletz d , Alexander Mellmann d , Willem van Schaik a , Ellen Brouwer a , Malbert Rogers a , Yvette Kraat e , Marc Bonten a , Jukka Corander f , Henrik Westh b , c , Dag Harmsen g and Rob J. L. Willems a a Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands b Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark c Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark d Institute of Hygiene, University of Münster, Münster, Germany e Department of Microbiology and Infection Prevention, Atrium-Orbis Medical Center, Sittard, the Netherlands f Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland g Department for Periodontology, University of Münster, Münster, Germany K. C. Carroll , Editor ABSTRACT Enterococcus faecium , a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium . However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium . cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.

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